A fundamental challenge in the drug discovery process is to develop drugs with high efficacy and minimal side- effects. As an initial step this depends on identifying lead compounds which interact with high affinity and regulate the activity of specific biological drug targets such as a protein involved in a disease pathway. However, a second equally important step is to verify that these leads do not interact and interfere with the functioning of the vast number of other proteins which comprise the human proteome. A variety of effective methods exist to perform label-free high throughput screening (HTS) of compound libraries against single drug targets. However, the ability to perform HTS on compound libraries, or even a small set of lead compounds, against a large library of protein targets has not yet emerged. Such high throughput multidimensional drug screening (HT-MDDS) would have a significant impact of the pharmaceutical and health- care industry. Most importantly, it would facilitate proteome-wide detection of off-target drug-protein interactions. Such interactions often cause serious adverse drug reactions (SADRs) responsible for the over 100,000 deaths per year in the U.S., exceeding the number of annual deaths due to cancer. In addition, HT-MDDS would provide a powerful method to discover new targets for existing FDA-approved drugs by identifying off-target interactions as well as to elucidate the molecular basis of side-effects fro on-label use. In order to meet this challenge, AmberGen has explored during Phase I the use of its proprietary Bead-GPS(tm) technology as a means to perform HT-MDDS during lead optimization. Bead-GPS(tm) is based on MALDI mass spectrometric imaging (MALDI-MSI) of high-density random bead-arrays, where each bead in the array carries a unique protein and corresponding photocleavable mass-tag for coding (PC-mass-tag). Binding of specific compounds to a specific protein is detected by measuring simultaneously the mass of the binders and the photoreleased PC-mass-tag(s) residing on each bead. Our initial results demonstrate the feasibility of using Bead- GPSTM to screen a drug compound library against thousands of proteins in order to rapidly identify both on- and off-target interactions on a global proteome-wide basis. Progress during Phase I included: i) Development of new photocleavable linkers for facile attachment of mass-tags to beads; ii) Demonstration of high capacity coding of protein-bead libraries with single and double PC-mass tags; iii) Construction of a model 50-member PC-mass-tag coded kinase library; iv) Screening the kinase bead-library with two known kinase inhibitors demonstrating 100% specificity and sensitivity. During Phase II, we will further optimize Bead-GPS(tm) for HT-MDDS with the goal of establishing it as a standard tool for pre-clinical lead optimization. For this purpose, we will construct a 400-member PC-mass-tagged kinase protein-bead library. This library will be screened by Bead-GPS(tm) against compounds from a model 373-member kinase inhibitor library. On-target and off-target interactions from positive hits detected by Bead-GPS(tm) will be further characterized for binding affinity and inhibitor activity using homogenous kinase assays, as well as by synchronization of fluorescent/FRET and MALDI-MS images of the random bead-array. Improvements in several aspects of the Bead-GPS(tm) process including advanced MALDI-MSI instrumentation and software will allow 5 to 10-fold improvements in sensitivity and scan speed. In order to accelerate the development and commercialization of Bead-GPS(tm), AmberGen will work closely with Dr. Cathy Costello, Director, Center for Biomedical Mass Spectrometry at the Boston University Medical School and a leading expert in the field of MALDI and its biomedical applications; Dr. Marvin Vestal, pioneer in MS- MALDI instrumentation development and President of SimulTOF Systems; Dr. Michael Pavia, a leader in the pharmaceutical industry and ex-CTO of Millennium Pharmaceuticals; Dr. Yiwu He, former Global Head and Senior Director of GlaxoSmithKline and currently Senior Program Officer at the Bill & Melinda Gates Foundation and Dr. Gheorghe Doros, Associate Professor of Biostatistics at the Boston University School of Public Health. AmberGen will also explore the use of improved MALDI-MSI instrumentation in collaboration with SimulTOF Systems and Bruker Daltonics.